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Conserved domains on  [gi|13357184|gb|AAK20033|]
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D,D-carboxypeptidase [Enterococcus faecium]

Protein Classification

D-alanyl-D-alanine carboxypeptidase family protein( domain architecture ID 11449003)

D-alanyl-D-alanine carboxypeptidase family protein such as Streptococcus pneumoniae L,D-carboxypeptidase Dacb and Enterococcus faecium D-alanyl-D-alanine carboxypeptidase, which removes C-terminal D-alanyl residues from sugar-peptide cell wall precursors

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LdcB COG1876
LD-carboxypeptidase LdcB, LAS superfamily [Cell wall/membrane/envelope biogenesis];
34-205 1.09e-63

LD-carboxypeptidase LdcB, LAS superfamily [Cell wall/membrane/envelope biogenesis];


:

Pssm-ID: 441480  Cd Length: 168  Bit Score: 194.71  E-value: 1.09e-63
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13357184  34 LVNRQNPIPAQYDVELEQlsNGERIDIRISPYLQDLFDAARTDGVYPIVASGYRTTEKQQEIMDEKIAEYkakgytsaqA 113
Cdd:COG1876   1 LVNKDHPLPADDLVPLPG--GGHRLRKEAAAAFEAMQAAAKKDGIDLVIVSGYRSYERQEALYNRKVARY---------G 69

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13357184 114 KAEAETWVAVPGTSEHQLGLAVDINADGIHSTGNE------VYRWLDENSYRFGFIRRYPPDKTEITGVSNEPWHYRYVG 187
Cdd:COG1876  70 IEAALRYSAPPGTSEHHTGLAIDIGDPDPGTDLEEefeetpAGKWLAANAAKYGFILRYPKGKEDITGYAYEPWHWRYVG 149

                       170
                ....*....|....*...
gi 13357184 188 IEAATEMYNQGVCLEEYL 205
Cdd:COG1876 150 VEAAKEIFEKGLTLEEYL 167
 
Name Accession Description Interval E-value
LdcB COG1876
LD-carboxypeptidase LdcB, LAS superfamily [Cell wall/membrane/envelope biogenesis];
34-205 1.09e-63

LD-carboxypeptidase LdcB, LAS superfamily [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 441480  Cd Length: 168  Bit Score: 194.71  E-value: 1.09e-63
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13357184  34 LVNRQNPIPAQYDVELEQlsNGERIDIRISPYLQDLFDAARTDGVYPIVASGYRTTEKQQEIMDEKIAEYkakgytsaqA 113
Cdd:COG1876   1 LVNKDHPLPADDLVPLPG--GGHRLRKEAAAAFEAMQAAAKKDGIDLVIVSGYRSYERQEALYNRKVARY---------G 69

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13357184 114 KAEAETWVAVPGTSEHQLGLAVDINADGIHSTGNE------VYRWLDENSYRFGFIRRYPPDKTEITGVSNEPWHYRYVG 187
Cdd:COG1876  70 IEAALRYSAPPGTSEHHTGLAIDIGDPDPGTDLEEefeetpAGKWLAANAAKYGFILRYPKGKEDITGYAYEPWHWRYVG 149

                       170
                ....*....|....*...
gi 13357184 188 IEAATEMYNQGVCLEEYL 205
Cdd:COG1876 150 VEAAKEIFEKGLTLEEYL 167
LD-carboxypeptidase cd14852
L,D-carboxypeptidase DacB and LdcB, and related proteins; This L,D-carboxypeptidase family ...
 33-194 4.59e-59

L,D-carboxypeptidase DacB and LdcB, and related proteins; This L,D-carboxypeptidase family includes LdcB LD-Carboxypeptidase from Streptococcus pneumoniae, Bacillus anthracis, and Bacillus subtilis, and L,D-carboxypeptidase DacB from Streptococcus pneumonia and Lactococcus lactis. These enzymes are active against cell-wall-derived tetrapeptides and synthetic tetrapeptides lacking the sugar moiety but are inactive against tetrapeptides terminating in L-alanine. L,D-carboxypeptidase DacB plays a key role in the remodeling of S. pneumoniae peptidoglycan during cell division. It adopts a zinc-dependent carboxypeptidase fold and acts as an L,D-carboxypeptidase towards the tetrapeptide L-Ala-D-iGln-L-Lys-D-Ala of the peptidoglycan stem. This family also includes vanY D-Ala-D-Ala carboxypeptidase which is vancomycin-inducible and penicillin-resistant. VanY hydrolyzes depsipeptide- and D-alanyl-D-alanine-containing peptidoglycan precursors; it is insensitive to beta-lactams. All these enzymes belong to the MEROPS family M15 subfamily B.


Pssm-ID: 350624  Cd Length: 162  Bit Score: 182.83  E-value: 4.59e-59
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13357184  33 ILVNRQNPIPAQYDVELEQ----LSNGERIDIRISPYLQDLFDAARTDGVYPIVASGYRTTEKQQEIMDEKIAEYKakgy 108
Cdd:cd14852   1 VLVNKDHPLPEDYVPEDLVpyvlLDNGLYLRKEAAEALEEMFDAAKKDGIDLTIVSGYRSYEYQQELYNNYVARYG---- 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13357184 109 tsaqaKAEAETWVAVPGTSEHQLGLAVDINADGIHSTGNEV-----YRWLDENSYRFGFIRRYPPDKTEITGVSNEPWHY 183
Cdd:cd14852  77 -----KEEADRYSARPGYSEHQTGLAVDIGSTDGPCLEESFedtpaGKWLAENAHKYGFILRYPKGKENITGYSYEPWHF 151

                       170
                ....*....|.
gi 13357184 184 RYVGIEAATEM 194
Cdd:cd14852 152 RYVGKEAAKKI 162
VanY pfam02557
D-alanyl-D-alanine carboxypeptidase;
55-188 3.17e-48

D-alanyl-D-alanine carboxypeptidase;


Pssm-ID: 426830 [Multi-domain]  Cd Length: 131  Bit Score: 153.93  E-value: 3.17e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13357184    55 GERIDIRISPYLQDLFDAARTDGVYPIVASGYRTTEKQQEIMDEkiaeykakgYTSAQAKAEAETWVAVPGTSEHQLGLA 134
Cdd:pfam02557   1 GIYLRKEAAEALEELFAAAKKEGINLRAISGFRSYEYQEALFKK---------YVKGEGKKAILRWSAPPGTSEHHTGLA 71

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 13357184   135 VDINADG------IHSTGNEVYRWLDENSYRFGFIRRYPPDKTEITGVSNEPWHYRYVGI 188
Cdd:pfam02557  72 IDIGDPDnpweleESFEDTAAFKWLQANAHKYGFVLRYPKGKEQITGVSYEPWHWRYVGI 131
 
Name Accession Description Interval E-value
LdcB COG1876
LD-carboxypeptidase LdcB, LAS superfamily [Cell wall/membrane/envelope biogenesis];
34-205 1.09e-63

LD-carboxypeptidase LdcB, LAS superfamily [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 441480  Cd Length: 168  Bit Score: 194.71  E-value: 1.09e-63
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13357184  34 LVNRQNPIPAQYDVELEQlsNGERIDIRISPYLQDLFDAARTDGVYPIVASGYRTTEKQQEIMDEKIAEYkakgytsaqA 113
Cdd:COG1876   1 LVNKDHPLPADDLVPLPG--GGHRLRKEAAAAFEAMQAAAKKDGIDLVIVSGYRSYERQEALYNRKVARY---------G 69

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13357184 114 KAEAETWVAVPGTSEHQLGLAVDINADGIHSTGNE------VYRWLDENSYRFGFIRRYPPDKTEITGVSNEPWHYRYVG 187
Cdd:COG1876  70 IEAALRYSAPPGTSEHHTGLAIDIGDPDPGTDLEEefeetpAGKWLAANAAKYGFILRYPKGKEDITGYAYEPWHWRYVG 149

                       170
                ....*....|....*...
gi 13357184 188 IEAATEMYNQGVCLEEYL 205
Cdd:COG1876 150 VEAAKEIFEKGLTLEEYL 167
LD-carboxypeptidase cd14852
L,D-carboxypeptidase DacB and LdcB, and related proteins; This L,D-carboxypeptidase family ...
 33-194 4.59e-59

L,D-carboxypeptidase DacB and LdcB, and related proteins; This L,D-carboxypeptidase family includes LdcB LD-Carboxypeptidase from Streptococcus pneumoniae, Bacillus anthracis, and Bacillus subtilis, and L,D-carboxypeptidase DacB from Streptococcus pneumonia and Lactococcus lactis. These enzymes are active against cell-wall-derived tetrapeptides and synthetic tetrapeptides lacking the sugar moiety but are inactive against tetrapeptides terminating in L-alanine. L,D-carboxypeptidase DacB plays a key role in the remodeling of S. pneumoniae peptidoglycan during cell division. It adopts a zinc-dependent carboxypeptidase fold and acts as an L,D-carboxypeptidase towards the tetrapeptide L-Ala-D-iGln-L-Lys-D-Ala of the peptidoglycan stem. This family also includes vanY D-Ala-D-Ala carboxypeptidase which is vancomycin-inducible and penicillin-resistant. VanY hydrolyzes depsipeptide- and D-alanyl-D-alanine-containing peptidoglycan precursors; it is insensitive to beta-lactams. All these enzymes belong to the MEROPS family M15 subfamily B.


Pssm-ID: 350624  Cd Length: 162  Bit Score: 182.83  E-value: 4.59e-59
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13357184  33 ILVNRQNPIPAQYDVELEQ----LSNGERIDIRISPYLQDLFDAARTDGVYPIVASGYRTTEKQQEIMDEKIAEYKakgy 108
Cdd:cd14852   1 VLVNKDHPLPEDYVPEDLVpyvlLDNGLYLRKEAAEALEEMFDAAKKDGIDLTIVSGYRSYEYQQELYNNYVARYG---- 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13357184 109 tsaqaKAEAETWVAVPGTSEHQLGLAVDINADGIHSTGNEV-----YRWLDENSYRFGFIRRYPPDKTEITGVSNEPWHY 183
Cdd:cd14852  77 -----KEEADRYSARPGYSEHQTGLAVDIGSTDGPCLEESFedtpaGKWLAENAHKYGFILRYPKGKENITGYSYEPWHF 151

                       170
                ....*....|.
gi 13357184 184 RYVGIEAATEM 194
Cdd:cd14852 152 RYVGKEAAKKI 162
VanY pfam02557
D-alanyl-D-alanine carboxypeptidase;
55-188 3.17e-48

D-alanyl-D-alanine carboxypeptidase;


Pssm-ID: 426830 [Multi-domain]  Cd Length: 131  Bit Score: 153.93  E-value: 3.17e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13357184    55 GERIDIRISPYLQDLFDAARTDGVYPIVASGYRTTEKQQEIMDEkiaeykakgYTSAQAKAEAETWVAVPGTSEHQLGLA 134
Cdd:pfam02557   1 GIYLRKEAAEALEELFAAAKKEGINLRAISGFRSYEYQEALFKK---------YVKGEGKKAILRWSAPPGTSEHHTGLA 71

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 13357184   135 VDINADG------IHSTGNEVYRWLDENSYRFGFIRRYPPDKTEITGVSNEPWHYRYVGI 188
Cdd:pfam02557  72 IDIGDPDnpweleESFEDTAAFKWLQANAHKYGFVLRYPKGKEQITGVSYEPWHWRYVGI 131
DD-dipeptidase_VanXYc cd14849
D-Ala-D-Ala dipeptidase/D-Ala-D-Ala carboxypeptidase (VanXYc) and related proteins; VanXYc ...
 66-187 1.05e-29

D-Ala-D-Ala dipeptidase/D-Ala-D-Ala carboxypeptidase (VanXYc) and related proteins; VanXYc peptidase (also known as vanXY(C) peptidase, D-alanyl-D-alanine carboxypeptidase D,D-dipeptidase/D,D-carboxypeptidase, vancomycin resistance D,D-dipeptidase) is a Zn2+-dependent enzyme that mediates resistance to the antibiotic vancomycin in Enterococci. Some of the vancomycin resistance operons encode VanXY D,D-carboxypeptidase which hydrolyzes both, dipeptide (D-Ala-D-Ala) or pentapeptide (UDP-MurNac-L-Ala-D-Glu-L-Lys-D-Ala-D-Ala). It is a bifunctional enzyme that catalyzes D,D-peptidase and D,D-carboxypeptidase activities. VanXY has higher sequence similarity to VanY than with VanX and hydrolyzes D,D-dipeptides such as D-Ala-D-Ala, whereas VanY is inactive against this substrate; thus having a less restrictive active site to accommodate larger substrates such as UDP-MurNAc-pentapeptide[Ala]. This family belongs to the MEROPS family M15, subfamily B, and includes the D,D-dipeptidases VanXYg and VanXYe.


Pssm-ID: 350623 [Multi-domain]  Cd Length: 127  Bit Score: 106.58  E-value: 1.05e-29
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13357184  66 LQDLFDAAR-TDGVYPIvaSGYRTTEKQQEIMDEKIAEyKAKGYTsaqakaeaETWVAVPGTSEHQLGLAVD--INADGI 142
Cdd:cd14849   9 LKKLLEAIGgEDEIVPV--SGYRSKEEQTAIYDDSLNE-NGEEFT--------EKYVALPGHSEHQTGLAIDlgLNKKDI 77

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|
gi 13357184 143 -----HSTGNEVYRWLDENSYRFGFIRRYPPDKTEITGVSNEPWHYRYVG 187
Cdd:cd14849  78 dficpSFPDSGICDLFREQAADYGFIERYPKDKEEITGISYEPWHFRYVG 127
Peptidase_M15 cd14814
Metalloproteases including zinc D-Ala-D-Ala carboxypeptidase, L-Ala-D-Glu peptidase, L, ...
 66-186 5.56e-29

Metalloproteases including zinc D-Ala-D-Ala carboxypeptidase, L-Ala-D-Glu peptidase, L,D-carboxypeptidase, bacteriophage endolysins, and related proteins; This family summarizes zinc-binding metallopeptidases which are mostly carboxypeptidases and dipeptidases, and includes zinc-dependent D-Ala-D-Ala carboxypeptidases, VanX, L-Ala-D-Glu peptidase, L,D-carboxypeptidase and bacteriophage endolysins, amongst other family members. These peptidases belong to MEROPS family M15 which are involved in bacterial cell wall biosynthesis and metabolism.


Pssm-ID: 350615 [Multi-domain]  Cd Length: 111  Bit Score: 104.45  E-value: 5.56e-29
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13357184  66 LQDLFDAARTDGVYPIVASGYRTTEKQQEIMDEKiaeykAKGYTSAqakaeaeTWVAVPGTSEHQLGLAVDINaDGIHST 145
Cdd:cd14814   7 LARMIAAAGAEGRTLTINSGYRTYAQQLRLFAAK-----GKGSGGR-------RWAAPPGTSNHQWGLAIDLG-DGGGWR 73

                        90       100       110       120
                ....*....|....*....|....*....|....*....|.
gi 13357184 146 GNEVYRWLDENSYRFGFIRRYPPDKteiTGVSNEPWHYRYV 186
Cdd:cd14814  74 ETQGYRWLKANAPRYGFDNPGGARR---GGAFQEPWHWEYV 111
Peptidase_M15_like cd14846
Uncharacterized family of the peptidase family M15, subfamily B; This family of ...
 66-185 4.63e-16

Uncharacterized family of the peptidase family M15, subfamily B; This family of uncharacterized proteins, similar to endolysin lys (Clavibacter phage CMP1) and VanYn peptidase, are zinc-binding enzymes that belong to the peptidase M15 subfamily B, involved in bacterial cell wall metabolism.


Pssm-ID: 350621  Cd Length: 104  Bit Score: 70.80  E-value: 4.63e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13357184  66 LQDLFDAARTDGVYPIVASGYRTTEKQQEIMDEKIAEYKakgytsaqAKAEAETWVAVPGTSEHQLGLAVDIN-ADGihs 144
Cdd:cd14846   9 LTAAATAAAADGVTLRITSGWRSPAEQQRLLDDAVRTYG--------SEEEARRWVAPPEDSAHVTGEAVDIGpADA--- 77

                        90       100       110       120
                ....*....|....*....|....*....|....*....|.
gi 13357184 145 tgnevYRWLDENSYRFGFIRRYppdkteitgvSNEPWHYRY 185
Cdd:cd14846  78 -----AQWLERHGARYGLCRIY----------ANEWWHFEL 103
DD-carboxypeptidase_like cd14847
Uncharacterized proteins of the MEROPS peptidase family M15, subfamily B; This family of ...
 66-185 1.22e-15

Uncharacterized proteins of the MEROPS peptidase family M15, subfamily B; This family of uncharacterized proteins similar to D-Ala-D-Ala carboxypeptidase pdcA (Myxococcus-type) are zinc-binding enzymes that belong to the peptidase M15 subfamily B. The enzyme D-Ala-D-Ala carbozypeptidase catalyzes carboxypeptidation reactions involved in bacterial cell wall metabolism.


Pssm-ID: 350622  Cd Length: 162  Bit Score: 71.07  E-value: 1.22e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13357184  66 LQDLFDAARTDGVYPIVASGYRTTEKQQEIMDEKIAEYKA----------KGYTSAQAKAEA-ETWVAVPGTSEHQLGLA 134
Cdd:cd14847   9 FLALQAAAAKDGFDLQIASSFRSFERQLAIWNRKWSGERPvlddngqpldISSLSPEEKIHAiLRWSALPGASRHHWGTD 88

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13357184 135 VDINA-------------------DGIhstGNEVYRWLDENSYRFGFIRRYPPDKteiTGVSNEPWHYRY 185
Cdd:cd14847  89 IDVYDanalpagyqlqltpseyeeGGP---FAKLYQWLDENAAKFGFFRPYTQDR---GGVAPEPWHLSY 152
L-Ala-D-Glu_peptidase_like cd14845
L-Ala-D-Glu peptidase, also known as L-alanyl-D-glutamate endopeptidase; This L-Ala-D-Glu ...
 56-138 7.52e-06

L-Ala-D-Glu peptidase, also known as L-alanyl-D-glutamate endopeptidase; This L-Ala-D-Glu peptidase family includes L-alanyl-D-glutamate peptidase (bacteriophage T5) (also known as L-alanoyl-D-glutamate endopeptidase), and Ply118 and Ply500 L-Ala-D-Glu peptidase. Bacteriophage endolysin degrades the peptidoglycan of the bacterial host from within, leading to cell lysis and release of progeny virions. The bacteriophage endolysin Ply118 cleaves between L-Ala and D-Glu residues of Listeria cell wall peptidoglycan. This family belongs to the MEROPS peptidase M15 subfamily C.


Pssm-ID: 350620 [Multi-domain]  Cd Length: 126  Bit Score: 43.89  E-value: 7.52e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13357184  56 ERIDIRISPYLQDLFDAARTDGVYPIVASGYRTTEKQqeimdekiAEYKAKGytsAQAKAEAETWvAVPGTSEHQLGLAV 135
Cdd:cd14845   6 AGLHPEVRAVVKELIELAEEEGIDFRITEGYRSPARQ--------AALYAQG---RTKPGLIVTN-ARGGQSYHNYGLAV 73


                ...
gi 13357184 136 DIN 138
Cdd:cd14845  74 DIV 76
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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